- Communication -

Volume 7

Full article

BRM-Parser: A tool for comprehensive analysis of BLAST and RepeatMasker results

Anjali Bajpai, Settu Sridhar, Hemakumar M. Reddy and Rachel A. Jesudasan*

Center for Cellular and Molecular Biology, Hyderabad - 500007, India


* Corresponding author
  Email: rachel@ccmb.res.in


Edited by E. Wingender; received October 05, 2006; revised February 28, 2007; accepted March 31, 2007; published April 22, 2007

Abstract

BLAST and RepeatMasker Parser (BRM-Parser) is a service that provides users a unified platform for easy analysis of relatively large outputs of BLAST (Basic Local Alignment Search Tool) and RepeatMasker programs. BLAST Summary feature of BRM-Parser summarizes BLAST outputs, which can be filtered using user defined thresholds for hit length, percentage identity and E-value and can be sorted by query or subject coordinates and length of the hit. It also provides a tool that merges BLAST hits which satisfy user-defined criteria for hit length and gap between hits. The RepeatMasker Summary feature uses the RepeatMasker alignment as an input file and calculates the frequency and proportion of mutations in copies of repeat elements, as identified by the RepeatMasker. Both features can be run through a GUI or can be executed via command line using the standalone version.

Keywords: BLAST, RepeatMasker, repeats, parse, filter, merge, mutation